Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets.

¹European Molecular Biology Laboratory, Heidelberg, FRG.

Computer Applications in the Biosciences : CABIOS

|February 1, 1992

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.

British journal of cancer·2009

Same author

Overlapping antisense transcription in the human genome.

Comparative and functional genomics·2008

Same author

Clustal W and Clustal X version 2.0.

Bioinformatics (Oxford, England)·2007

Same author

Mind the gaps: progress in progressive alignment.

Proceedings of the National Academy of Sciences of the United States of America·2005

Same author

Getting better with bifidobacteria.

Journal of applied microbiology·2005

Same author

Multiple sequence alignment.

Methods in molecular biology (Clifton, N.J.)·2000

Same journal

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

Computer applications in the biosciences : CABIOS·1998

Same journal

Two applications to facilitate the viewing of database search result files on the Macintosh.

Computer applications in the biosciences : CABIOS·1998

Same journal

BioWish: a molecular biology command extension to Tcl/Tk.

Computer applications in the biosciences : CABIOS·1998

Same journal

The Sequence Alerting Server--a new WEB server.

Computer applications in the biosciences : CABIOS·1998

Same journal

A software tool for the analysis of mass spectrometric disulfide mapping experiments.

Computer applications in the biosciences : CABIOS·1998

Same journal

SAMBA: hardware accelerator for biological sequence comparison.

Computer applications in the biosciences : CABIOS·1998

See all related articles

Principal coordinates analysis offers a novel approach for sequence analysis, visualizing complex data by creating low-dimensional representations of sequence distance matrices. This method enhances understanding of sequence relationships and complements phylogenetic analyses.

Area of Science:

Bioinformatics
Computational Biology
Sequence Analysis

Background:

Ordination is a powerful data analysis technique largely underutilized in sequence analysis.
Principal coordinates analysis (PCoA) can represent complex datasets in lower dimensions.

Purpose of the Study:

To demonstrate the application of principal coordinates analysis (PCoA) for analyzing aligned sequence data.
To explore the utility of PCoA in uncovering relationships within sequence datasets.

Main Methods:

Utilizing PCoA to generate low-dimensional representations from distance matrices of aligned sequences.
Calculating Euclidean distances between sequences, with a focus on the square root of percentage difference, while considering the impact of gaps.

Related Experiment Videos

Main Results:

PCoA successfully represented known relationships in a dataset of 226 aligned globins.
Analysis of 610 aligned 5S rRNA sequences demonstrated the method's applicability to different sequence types.

Conclusions:

Sequence ordination using PCoA provides a valuable complement to traditional phylogenetic analyses.
PCoA offers a complementary visualization and analysis tool for sequence data, rather than a replacement for existing methods.